--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/misc/maq2sam.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,173 @@
+#include <string.h>
+#include <zlib.h>
+#include <stdio.h>
+#include <inttypes.h>
+#include <stdlib.h>
+#include <assert.h>
+
+#define PACKAGE_VERSION "r439"
+
+//#define MAQ_LONGREADS
+
+#ifdef MAQ_LONGREADS
+#  define MAX_READLEN 128
+#else
+#  define MAX_READLEN 64
+#endif
+
+#define MAX_NAMELEN 36
+#define MAQMAP_FORMAT_OLD 0
+#define MAQMAP_FORMAT_NEW -1
+
+#define PAIRFLAG_FF      0x01
+#define PAIRFLAG_FR      0x02
+#define PAIRFLAG_RF      0x04
+#define PAIRFLAG_RR      0x08
+#define PAIRFLAG_PAIRED  0x10
+#define PAIRFLAG_DIFFCHR 0x20
+#define PAIRFLAG_NOMATCH 0x40
+#define PAIRFLAG_SW      0x80
+
+typedef struct
+{
+	uint8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
+	uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
+	uint32_t seqid, pos;
+	int dist;
+	char name[MAX_NAMELEN];
+} maqmap1_t;
+
+typedef struct
+{
+	int format, n_ref;
+	char **ref_name;
+	uint64_t n_mapped_reads;
+	maqmap1_t *mapped_reads;
+} maqmap_t;
+
+maqmap_t *maq_new_maqmap()
+{
+	maqmap_t *mm = (maqmap_t*)calloc(1, sizeof(maqmap_t));
+	mm->format = MAQMAP_FORMAT_NEW;
+	return mm;
+}
+void maq_delete_maqmap(maqmap_t *mm)
+{
+	int i;
+	if (mm == 0) return;
+	for (i = 0; i < mm->n_ref; ++i)
+		free(mm->ref_name[i]);
+	free(mm->ref_name);
+	free(mm->mapped_reads);
+	free(mm);
+}
+maqmap_t *maqmap_read_header(gzFile fp)
+{
+	maqmap_t *mm;
+	int k, len;
+	mm = maq_new_maqmap();
+	gzread(fp, &mm->format, sizeof(int));
+	if (mm->format != MAQMAP_FORMAT_NEW) {
+		if (mm->format > 0) {
+			fprintf(stderr, "** Obsolete map format is detected. Please use 'mapass2maq' command to convert the format.\n");
+			exit(3);
+		}
+		assert(mm->format == MAQMAP_FORMAT_NEW);
+	}
+	gzread(fp, &mm->n_ref, sizeof(int));
+	mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
+	for (k = 0; k != mm->n_ref; ++k) {
+		gzread(fp, &len, sizeof(int));
+		mm->ref_name[k] = (char*)malloc(len * sizeof(char));
+		gzread(fp, mm->ref_name[k], len);
+	}
+	/* read number of mapped reads */
+	gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
+	return mm;
+}
+
+void maq2tam_core(gzFile fp, const char *rg)
+{
+	maqmap_t *mm;
+	maqmap1_t mm1, *m1;
+	int ret;
+	m1 = &mm1;
+	mm = maqmap_read_header(fp);
+	while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
+		int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
+		if (m1->flag) flag |= 1;
+		if ((m1->flag&PAIRFLAG_PAIRED) || ((m1->flag&PAIRFLAG_SW) && m1->flag != 192)) flag |= 2;
+		if (m1->flag == 192) flag |= 4;
+		if (m1->flag == 64) flag |= 8;
+		if (m1->pos&1) flag |= 0x10;
+		if ((flag&1) && m1->dist != 0) {
+			int c;
+			if (m1->dist > 0) {
+				if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_RF)) c = 0;
+				else if (m1->flag&(PAIRFLAG_FR|PAIRFLAG_RR)) c = 1;
+				else c = m1->pos&1;				
+			} else {
+				if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_FR)) c = 0;
+				else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
+				else c = m1->pos&1;
+			}
+			if (c) flag |= 0x20;
+		}
+		if (m1->flag) {
+			int l = strlen(m1->name);
+			if (m1->name[l-2] == '/') {
+				flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;
+				m1->name[l-2] = '\0';
+			}
+		}
+		printf("%s\t%d\t", m1->name, flag);
+		printf("%s\t%d\t", mm->ref_name[m1->seqid], (m1->pos>>1)+1);
+		if (m1->flag == 130) {
+			int c = (int8_t)m1->seq[MAX_READLEN-1];
+			printf("%d\t", m1->alt_qual);
+			if (c == 0) printf("%dM\t", m1->size);
+			else {
+				if (c > 0) printf("%dM%dI%dM\t", m1->map_qual, c, m1->size - m1->map_qual - c);
+				else printf("%dM%dD%dM\t", m1->map_qual, -c, m1->size - m1->map_qual);
+			}
+			se_mapq = 0; // zero SE mapQ for reads aligned by SW
+		} else {
+			if (flag&4) printf("0\t*\t");
+			else printf("%d\t%dM\t", m1->map_qual, m1->size);
+		}
+		printf("*\t0\t%d\t", m1->dist);
+		for (j = 0; j != m1->size; ++j) {
+			if (m1->seq[j] == 0) putchar('N');
+			else putchar("ACGT"[m1->seq[j]>>6&3]);
+		}
+		putchar('\t');
+		for (j = 0; j != m1->size; ++j)
+			putchar((m1->seq[j]&0x3f) + 33);
+		putchar('\t');
+		if (rg) printf("RG:Z:%s\t", rg);
+		if (flag&4) { // unmapped
+			printf("MF:i:%d\n", m1->flag);
+		} else {
+			printf("MF:i:%d\t", m1->flag);
+			if (m1->flag) printf("AM:i:%d\tSM:i:%d\t", m1->alt_qual, se_mapq);
+			printf("NM:i:%d\tUQ:i:%d\tH0:i:%d\tH1:i:%d\n", m1->info1&0xf, m1->info2, m1->c[0], m1->c[1]);
+		}
+	}
+	if (ret > 0)
+		fprintf(stderr, "Truncated! Continue anyway.\n");
+	maq_delete_maqmap(mm);
+}
+
+int main(int argc, char *argv[])
+{
+	gzFile fp;
+	if (argc == 1) {
+		fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+		fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
+		return 1;
+	}
+	fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
+	maq2tam_core(fp, argc > 2? argv[2] : 0);
+	gzclose(fp);
+	return 0;
+}